Online
Jul 26-30, 2021
1 pm - 5 pm UTC+1
Instructors: Uma Arora, Annajiat Alim Rasel, Jannetta Steyn
Helpers: helper one, helper two
Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".
Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.
When: Jul 26-30, 2021. Add to your Google Calendar.
Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).
Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.
Contact: Please email hn7@sanger.ac.uk for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Please be sure to complete these surveys before and after the workshop.
1 | Date | Day | Time | Duration | Lesson | Episode | |
|---|---|---|---|---|---|---|---|
2 | 26 July | 1 | 13:00 | 00:15 | Housekeeping (15 minutes) | ||
3 | 13:15 | 00:30 | Project Organization and Management | 1 | Data Tidiness (30 minutes) | ||
4 | 13:45 | 00:15 | 2 | Planning for NGS Projects (30 minutes) | |||
5 | 14:00 | 00:15 | BREAK (15 minutes) | ||||
6 | 14:15 | 00:15 | 2 | Planning for NGS Projects | |||
7 | 14:30 | 00:30 | 3 | Examining Data on the NCBI SRA Database (30 minutes) | |||
8 | 15:00 | 00:30 | Introduction to the Command Line | 1 | Introducing the Shell (30 minutes) | ||
9 | 15:30 | 00:15 | BREAK (15 minutes) | ||||
10 | 15:45 | 00:50 | 2 | Navigating Files and Directories (50 minutes) | |||
11 | 16:35 | End of Day 1 | |||||
12 | |||||||
13 | 27 July | 2 | 13:00 | 00:15 | HouseKeeping (15 minutes) | ||
14 | 13:15 | 00:45 | Introduction to the Command Line | 3 | Working with Files and Directories (45 minutes) | ||
15 | 14:00 | 00:15 | 4 | Redirection (45 minutes) | |||
16 | 14:15 | 00:15 | BREAK (15 minutes) | ||||
17 | 14:30 | 00:30 | 4 | Redirection | |||
18 | 15:00 | 00:40 | 5 | Writing Scripts and Working with Data (40 minutes) | |||
19 | 15:40 | 00:15 | BREAK (15 minutes) | ||||
20 | 15:55 | 00:30 | 6 | Project Organization (30 minutes) | |||
21 | 16:25 | 00:15 | Data Wrangling and Processing | 1 | Background and Metadata (15 minutes) | ||
22 | 16:40 | 00:15 | 2 | Assessing Read Quality (50 minutes) | |||
23 | 16:55 | End of Day 2 | |||||
24 | |||||||
25 | 28 July | 3 | 13:00 | 00:15 | Housekeeping (15 minutes) | ||
26 | 13:15 | 00:45 | Data Wrangling and Processing | 2 | Assessing Read Quality | ||
27 | 14:00 | 00:30 | 3 | Trimming and Filtering (55 minutes) | |||
28 | 14:30 | 00:15 | BREAK (15 minutes) | ||||
29 | 14:45 | 00:25 | 3 | Trimming and Filtering | |||
30 | 15:10 | 00:30 | 4 | Variant Calling Workflow (60 minutes) | |||
31 | 15:40 | 00:15 | BREAK (15 minutes) | ||||
32 | 15:55 | 00:30 | 4 | Variant Calling Workflow | |||
33 | 16:25 | 00:20 | 5 | Automating a Variant Calling Workflow (45 minutes) | |||
34 | 16:45 | End of Day 3 | |||||
35 | |||||||
36 | 29 July | 4 | 13:00 | 00:15 | Housekeeping (15 minutes) | ||
37 | 13:15 | 00:25 | Data Wrangling and Processing | 5 | Automating a Variant Calling Workflow | ||
38 | 13:40 | 00:05 | Introduction to Cloud Computing for Genomics | 1 | Why Cloud Computing (5 minutes) | ||
39 | 13:45 | 00:10 | 2 | Logging onto the Cloud (10 minutes) | |||
40 | 13:55 | 00:15 | 3 | Fine Tuning Your Cloud Setup (15 minutes) | |||
41 | 14:10 | 00:30 | 4 | Which Cloud For My Data (30 minutes) | |||
42 | 14:40 | 00:15 | Intro to R and RStudio for Genomics | BREAK (15 minutes) | |||
43 | 14:55 | 00:45 | 1 | Introducing R and RStudio IDE (45 minutes) | |||
44 | 15:40 | 00:15 | 2 | R Basics (80 minutes) | |||
45 | 15:55 | 00:15 | BREAK (15 minutes) | ||||
46 | 16:10 | 00:45 | 2 | R Basics | |||
47 | 16:55 | End of Day 4 | |||||
48 | |||||||
49 | 30 July | 5 | 13:00 | 00:05 | Housekeeping (15 minutes) | ||
50 | 13:05 | 00:20 | Intro to R and RStudio for Genomics | 2 | R Basics | ||
51 | 13:05 | 01:00 | 3 | R Basics continued - factors and data frames (90 minutes) | |||
52 | 14:05 | 00:15 | BREAK (15 minutes) | ||||
53 | 14:20 | 00:30 | 3 | R Basics continued - factors and data frames | |||
54 | 14:50 | 00:55 | 4 | Aggregating and Analyzing Data with dplyr (55 minutes) | |||
55 | 15:45 | 00:15 | BREAK (15 minutes) | ||||
56 | 16:00 | 00:45 | 5 | Data Visualization with ggplot2 (90 minutes) | |||
57 | 16:45 | 00:15 | Complete Post-workshop Survey | End of Day 5 | |||
58 | 17:00 | 5 | Data Visualization with ggplot2 | ||||
59 | 17:00 | ||||||
60 | 17:00 | XX | Producing Reports With knitr (75 minutes) | ||||
61 | 17:00 |
To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.
Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:
The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site
.